get_transcriptome_id_from_phenotype_id {avidaR}

Get transcriptome from phenotype

Description

Get the transcriptome of a digital organism whose genome encodes a specific phenotype for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_id_from_phenotype_id(
  phenotype_id,
  seed_id = sample(1:1000, 1),
  transcriptome_seq = FALSE,
  transcriptome_pos = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

phenotype_id

Integer or list of integer values.

seed_id

Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000).

transcriptome_seq

Logical value (TRUE/FALSE) to show/hide this column (FALSE by default).

transcriptome_pos

Logical value (TRUE/FALSE) to show/hide this column (FALSE by default).

phenotype_binary

Logical value (TRUE/FALSE) to show/hide this column (FALSE by default).

triplestore

Object of class triplestore_access which manages database access.

Value

Data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional), "phenotype_id", "phenotype_binary" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single phenotype
get_transcriptome_id_from_phenotype_id(
  phenotype_id = 1,
  transcriptome_seq = TRUE,
  triplestore = avidaDB
)

# More than one phenotype at seed_1
get_transcriptome_id_from_phenotype_id(
  phenotype_id = c(1, 2), seed_id = 1,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_transcriptome_id_from_phenotype_id(
  phenotype_id = 1,
  seed_id = c(1, 2),
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)